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Showing :
comBat
•
reset
0
votes
0
replies
73
views
can ENmix::oxBS.MLE be run on comBat-adjusted data?
ENmix
comBat
10 days ago
joannew
• 0
0
votes
3
replies
118
views
ComBat Normalisation - data is integers and some floats, confused?!
combat
rnaseq
combatnormalisation
jeffleek
sva
updated 4 weeks ago by
Kevin Blighe
2.7k • written 4 weeks ago by
zeegzaag
• 0
1
vote
8
replies
252
views
Error in running Combat function
sva
ComBat
updated 10 weeks ago by
Kevin Blighe
2.7k • written 12 weeks ago by
Reza
▴ 10
0
votes
5
replies
108
views
Variable of interest in combat correction
sva
combat
updated 5 months ago by
James W. MacDonald
56k • written 5 months ago by
ch_el
▴ 10
0
votes
3
replies
149
views
Extracting a subset of samples following SVA
Combat
SVA
Limma
updated 6 months ago by
Kevin Blighe
2.7k • written 6 months ago by
jonellevillar
• 0
7
votes
6
replies
178
views
sva ComBat implementation for multiple sources of batch effects
sva
combat
batch-adjustment
updated 11 months ago by
W. Evan Johnson
▴ 840 • written 11 months ago by
Zach Roe
▴ 10
1
vote
2
replies
128
views
Validity of duplicateCorrelation after ComBat in this scenario
limma
ComBat
SVA
updated 14 months ago by
Gordon Smyth
42k • written 14 months ago by
vizio12341337
• 0
0
votes
0
replies
317
views
adjusting for batch using ComBat (sva) - singularity error
microarray
combat
sva
batch effects
15 months ago
anne.bozack
• 0
0
votes
1
reply
113
views
Batch correction in Linear Models for methylation data
methylation
ComBat
Linear models
batch correction
AIC
updated 16 months ago by
Kevin Blighe
2.7k • written 16 months ago by
lucasmiranda42
• 0
0
votes
1
reply
154
views
problem for interpretation of resulted ComBat() plot
ComBat
sva
batch effect
RNA-seq
updated 16 months ago by
W. Evan Johnson
▴ 840 • written 16 months ago by
modarzi
▴ 10
0
votes
3
replies
188
views
In SVA, the percent of biological variable of interest didnot change after adding SV1
SVA
combat
r
microarray
covariates
updated 17 months ago by
Martin Morgan
25k • written 17 months ago by
dhwani2410
• 0
4
votes
18
replies
2.9k
views
Batch correction by using ComBat function in sva package
deseq2
combat
Knownbatcheffect
Tutorial
updated 7 weeks ago by
Samuel Daniel
• 0 • written 18 months ago by
rajeshparmar4
• 0
2
votes
2
replies
240
views
Modelling a multiplicative batch effect with DESeq2
deseq2
batch-effects
ComBat
updated 18 months ago by
Michael Love
32k • written 18 months ago by
Sam
▴ 10
2
votes
3
replies
235
views
Design for introducing batch effect in DESeq2
deseq2
combat
batch effect
rna-seq
edger
updated 19 months ago by
swbarnes2
▴ 670 • written 19 months ago by
ag1805x
▴ 50
0
votes
2
replies
173
views
Analyzing a RNA-Seq dataset with paired samples and 2 batches
deseq2
sva
combat
updated 19 months ago by
Michael Love
32k • written 19 months ago by
ege.dedeoglu
• 0
0
votes
0
replies
206
views
The correct specification of the model matrix to ComBat
ComBat
sva
20 months ago
Sam
▴ 10
0
votes
6
replies
649
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma
deseq2
edger
scRNAseq
combat
updated 20 months ago by
Andrew_McDavid
▴ 260 • written 20 months ago by
Bogdan
▴ 610
7
votes
4
replies
1.2k
views
correcting the batch effects in Limma and SVA
limma
combat
sva
updated 20 months ago by
Gordon Smyth
42k • written 20 months ago by
Bogdan
▴ 610
4
votes
16
replies
320
views
How should I compare two different RNA-seq datasets using DESeq2 or EgdeR?
deseq2
limma
combat
updated 22 months ago by
Michael Love
32k • written 22 months ago by
joseale2310
▴ 10
3
votes
12
replies
831
views
ComBat normalization for batch effect change 0 values
ComBat
batch effect
sva
normalization
updated 23 months ago by
James W. MacDonald
56k • written 23 months ago by
hackingfactory
▴ 10
0
votes
0
replies
299
views
ComBat: missing peptide for one batch
batch effect
missing value
Combat
updated 2.5 years ago by
Gordon Smyth
42k • written 2.5 years ago by
hjleeab
• 0
0
votes
2
replies
546
views
DESeq2 batch correction and possible ComBat/SVA over-correction of RNA-seq data
deseq2
combat
sva
rna-seq
updated 2.6 years ago by
Michael Love
32k • written 2.6 years ago by
grimmerucsf
• 0
0
votes
0
replies
302
views
ComBat covariate bias when building centroid based predictors
combat
combat sva
pamr
limma design matrix
sva
2.6 years ago
jmsendoya
• 0
0
votes
1
reply
540
views
A problem in using Combat
sva
combat
updated 2.8 years ago by
W. Evan Johnson
▴ 840 • written 2.8 years ago by
linw
• 0
1
vote
1
reply
1.4k
views
Unexpected clustering of samples after batch effect removal with ComBat
ComBat
updated 3.2 years ago by
Gordon Smyth
42k • written 6.1 years ago by
jaro.slamecka
▴ 130
1
vote
9
replies
980
views
Removing batch effects from microarray data based on only a subset of samples
limma
removebatcheffect()
ComBat
microarray
3.2 years ago
jaro.slamecka
▴ 130
0
votes
8
replies
1.1k
views
Combat in gene pattern error annotation
software error
ComBat
Gene Pattern
updated 3.3 years ago by
shaymaa_s_elgaafary
• 0 • written 5.7 years ago by
radhikaraheja
• 0
0
votes
0
replies
462
views
SVA/Combat without fitting an intercept
sva
combat
batch effect
limma
3.5 years ago
elim
• 0
0
votes
1
reply
435
views
Combat prior plots good enough?
combat
combat sva
3.5 years ago
Miss Agnieszka Aleksandra Golicz
▴ 40
2
votes
5
replies
981
views
Running ComBat Without a Batch Argument to Correct for Continuous, Numeric Covariates
combat
sva
updated 3.5 years ago by
W. Evan Johnson
▴ 840 • written 3.5 years ago by
JMallory
• 0
1
vote
5
replies
2.3k
views
RNA-Seq Batch correction negative values
rna-seq
batch-effect
combat
scran
sva
updated 3.5 years ago by
Aaron Lun
★ 26k • written 3.5 years ago by
rmf
▴ 20
1
vote
1
reply
1.1k
views
Adjusting batch effects in microarray expression data using empirical Bayes methods
ComBat
microarray
batch effects
updated 3.7 years ago by
James W. MacDonald
56k • written 3.7 years ago by
DataFanatic
• 0
0
votes
0
replies
809
views
Data format after removing batch effects using linear model vs using comBat
microarray
SVA
ComBat
Linear models
Residuals
3.7 years ago
DataFanatic
• 0
0
votes
4
replies
1.2k
views
DESeq2, outlier correction, Combat, NMF
deseq2
combat
outliers
NMF
updated 3.9 years ago by
Michael Love
32k • written 3.9 years ago by
noname
• 0
0
votes
0
replies
659
views
Putative batch effect assessment and correction for downstream DE analysis with microarray dataset
hta2.0
limma
batch effect
affymetrix microarrays
ComBat
3.9 years ago
svlachavas
▴ 780
1
vote
1
reply
509
views
How to interpret the SVA results
SVA
combat
RNA-seq
updated 4.0 years ago by
James W. MacDonald
56k • written 4.0 years ago by
xie186
• 0
8
votes
4
replies
1.3k
views
Adjust for multiple batches using combat
combat
sva
limma
updated 4.1 years ago by
Aaron Lun
★ 26k • written 4.1 years ago by
juls
• 0
3
votes
4
replies
1.3k
views
How to normalize chromatin and RNA-Seq data together ?
atac-seq
atac
deseq2
sva
combat
updated 4.1 years ago by
Michael Love
32k • written 4.1 years ago by
g.atla
▴ 10
0
votes
0
replies
514
views
How can I evaluate whether ComBat's parametric prior is appropriate for my data?
combat
rnaseq
sva
4.2 years ago
Ryan C. Thompson
7.6k
0
votes
6
replies
640
views
Combine RNAseq datasets vst + Combat
combat
vst
deseq2
4.5 years ago
User34591
• 0
4
votes
2
replies
5.4k
views
ComBat to remove batch effects from RNA Seq data
combat
rnaseq
updated 4.5 years ago by
polemiraza
▴ 60 • written 4.5 years ago by
kerrypop
▴ 20
5
votes
3
replies
2.1k
views
about SVA: matrix of corrected expression values
SVA
COMBAT
4.5 years ago
Bogdan
▴ 610
3
votes
8
replies
1.1k
views
What type of data normalization for multiple microarrays?
normalization
microarray
combat
updated 4.6 years ago by
manimaran_1975
▴ 30 • written 4.6 years ago by
Ewelina Dratkiewicz
• 0
13
votes
2
replies
2.1k
views
voom with combat
limma
voom
combat
batch effect
updated 4.7 years ago by
Gordon Smyth
42k • written 4.7 years ago by
eldronzhou
▴ 10
0
votes
1
reply
554
views
Appropriate input of merged datasets regarding batch effect correction with ComBat in R
microarray
batcheffectcorrection
affymetrix microarrays
ComBat
sva
updated 4.7 years ago by
chris86
▴ 390 • written 4.8 years ago by
svlachavas
▴ 780
44
votes
20
replies
24k
views
Batch correction in DESeq2
rnaseq
batch effect
deseq2
combat
removebatcheffect()
updated 4.9 years ago by
adam
• 0 • written 5.3 years ago by
AB
▴ 100
2
votes
3
replies
749
views
comBat/SVA with no "variable of interest" and two batches
combat
sva
covariates
updated 4.9 years ago by
chris86
▴ 390 • written 5.0 years ago by
TP
• 0
0
votes
0
replies
559
views
SVA: Using ComBat for synthetic genetic array data
combat sva
sga
combat
batch effect
5.0 years ago
John Townsend
▴ 20
7
votes
3
replies
2.1k
views
SVA: Including variable of interest in ComBat model matrix
combat sva
SVA
sva
ComBat
batch effect
updated 5.0 years ago by
W. Evan Johnson
▴ 840 • written 5.0 years ago by
John Townsend
▴ 20
10
votes
10
replies
2.4k
views
Method for batch correction
combat
sva
limma
updated 5.0 years ago by
Vegard Nygaard
▴ 110 • written 5.0 years ago by
AST
▴ 50
77 results • Page
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Comment: RSamtools idxstatsBam not working with remote bam file
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Answer: RSamtools idxstatsBam not working with remote bam file
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Hi Jeremy. We got it and we are working on the issue. Thanks for your patience. A
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